Quest for Orthologs Entails Quest for Tree of Life: In Search of the Gene Stream

Brigitte Boeckmann, Marina Marcet-Houben, Jonathan A. Rees, Kristoffer Forslund, Jaime Huerta-Cepas, Matthieu Muffato, Pelin Yilmaz, Ioannis Xenarios, Peer Bork, Suzanna E. Lewis, Toni Gabaldón

Quest for Orthologs (QfO) is a community effort with the goal to improve and benchmark orthology predictions. As quality assessment assumes prior knowledge on species phylogenies, we investigated the congruency between existing species trees by comparing the relationships of 147 QfO reference organisms from six Tree of Life (ToL) / species tree projects: the NCBI taxonomy, Opentree of Life, the sequenced species/species Tree of Life (sToL), the 16S rRNA database, and trees published by Ciccarelli et al in 2006, and by Huerta-Cepas et al in 2014. Our study reveals that each species tree suggests a different phylogeny: 87 out of 146 (60%) possible splits of a dichotomous and rooted tree are congruent, while all other splits are incongruent in at least one of the species trees. Topological differences are observed not only at deep speciation events, but also within younger clades, such as Hominidae, Rodentia, Laurasiatheria, or rosids. The evolutionary relationships of 27 archaea and bacteria are highly inconsistent. By assessing 458,108 gene trees from 65 genomes we show that consistent species topologies are more often supported by gene phylogenies than contradicting ones. The largest concordant species tree includes 77 of the QfO reference organisms at the most. Results are summarized in the form of a consensus ToL (http://swisstree.vital-it.ch/species_tree) that can serve different benchmarking purposes.